Variant report

Variant	rs12076788
Chromosome Location	chr1:224355701-224355702
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10753454	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10799478	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10799480	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799505	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916320	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10916355	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916367	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916371	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916403	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916415	0.83[ASN][1000 genomes]
rs11808787	0.82[AMR][1000 genomes]
rs12038372	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12049583	0.81[ASN][1000 genomes]
rs12070670	0.85[ASN][1000 genomes]
rs12563153	0.83[ASN][1000 genomes]
rs12730611	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13374070	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1492694	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16844819	0.83[ASN][1000 genomes]
rs17560970	0.82[ASN][1000 genomes]
rs1826421	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2014782	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2051105	0.81[ASN][1000 genomes]
rs2172361	0.81[ASN][1000 genomes]
rs2280291	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2404843	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2896985	0.82[ASN][1000 genomes]
rs3767730	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3820482	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3820483	0.82[ASN][1000 genomes]
rs4653563	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653564	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4653972	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4653986	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653991	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653995	0.81[ASN][1000 genomes]
rs55664906	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55736782	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61827699	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426139	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6426143	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426169	0.85[ASN][1000 genomes]
rs66506223	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6657467	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6658494	0.82[ASN][1000 genomes]
rs6659234	0.82[ASN][1000 genomes]
rs6680651	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6682551	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685405	0.83[AMR][1000 genomes]
rs6685783	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6688818	0.81[ASN][1000 genomes]
rs6691405	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6698041	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6700284	0.83[AMR][1000 genomes]
rs7511895	0.81[ASN][1000 genomes]
rs7518839	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7524705	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526252	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7531891	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7542293	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7546235	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8328	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs869945	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs908795	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs997296	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs997297	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12076788	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12076788	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224327600-224356400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:224339200-224363200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:224345400-224363400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:224345600-224363400	Weak transcription	Ovary	ovary
6	chr1:224345800-224356600	Weak transcription	Small Intestine	intestine
7	chr1:224346000-224356600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:224346200-224356000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:224346200-224356600	Weak transcription	NHLF	lung
10	chr1:224346400-224356600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:224346400-224370000	Weak transcription	Esophagus	oesophagus
12	chr1:224346600-224356400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:224346600-224356400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:224346600-224356400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:224346600-224356600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:224346600-224356600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:224346600-224356600	Weak transcription	Aorta	Aorta
18	chr1:224346600-224356600	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:224346600-224356600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:224346600-224356600	Weak transcription	Thymus	Thymus
21	chr1:224346600-224356600	Weak transcription	HSMMtube	muscle
22	chr1:224346600-224358200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:224346600-224363200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:224346600-224363200	Weak transcription	Fetal Stomach	stomach
25	chr1:224346600-224363400	Weak transcription	Right Ventricle	heart
26	chr1:224346600-224363400	Weak transcription	Spleen	Spleen
27	chr1:224346800-224356400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:224346800-224356400	Weak transcription	NHEK	skin
29	chr1:224346800-224356600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:224346800-224356600	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:224346800-224356600	Weak transcription	Psoas Muscle	Psoas
32	chr1:224347000-224356200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:224347200-224356400	Weak transcription	HepG2	liver
34	chr1:224347200-224356600	Weak transcription	GM12878-XiMat	blood
35	chr1:224347400-224356000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:224347600-224356000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:224347600-224356400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:224347600-224356400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:224348000-224356600	Weak transcription	HMEC	breast
40	chr1:224348000-224356600	Weak transcription	NHDF-Ad	bronchial
41	chr1:224348200-224356200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:224348200-224356400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:224348200-224356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:224348200-224356600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:224348200-224356600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:224348200-224358000	Weak transcription	Hela-S3	cervix
47	chr1:224348400-224356000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:224348400-224356000	Weak transcription	Fetal Thymus	thymus
49	chr1:224348400-224356400	Weak transcription	Primary T cells from cord blood	blood
50	chr1:224348400-224356400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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